three_pos_results

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Last updated: 2025-02-11

Checks: 7 0

Knit directory: LSCI_pipeline/

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---

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Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    data/1kgp/
    Ignored:    data/hgdp/
    Ignored:    data/reference/
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Unstaged changes:
    Modified:   README.md
    Modified:   code/batch_c_v_c.sh
    Modified:   code/batch_single_pos.sh
    Modified:   code/batch_single_pos_stat.sh
    Modified:   code/sample_control.py
    Modified:   code/single_position_models.py
    Modified:   code/single_position_models_posOnly.py
    Modified:   code/sp_control_v_control.py
    Modified:   code/sp_control_v_control_v2.py
    Modified:   code/two_position_model.py
    Modified:   code/two_position_resid.py

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File	Version	Author	Date	Message
Rmd	2a9484f	Andy Beck	2025-02-11	wflow_publish("analysis/three_pos_results.Rmd")
html	05d7220	Andy Beck	2025-02-04	Build site.
Rmd	952e1b7	Andy Beck	2025-02-04	wflow_publish("analysis/three_pos_results.Rmd")
html	b1d3781	Andy Beck	2025-02-04	Build site.
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Rmd	4d83939	Andy Beck	2025-02-04	wflow_publish("analysis/three_pos_results.Rmd")
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Rmd	fed7f04	Andy Beck	2025-02-04	wflow_publish("analysis/three_pos_results.Rmd")
html	ee982ca	Andy Beck	2025-02-04	Build site.
Rmd	4edf50d	Andy Beck	2025-02-04	wflow_publish("analysis/three_pos_results.Rmd")
html	38e6b51	Andy Beck	2025-02-04	Build site.
Rmd	1311496	Andy Beck	2025-02-04	wflow_publish("analysis/three_pos_results.Rmd")
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Rmd	4221d4d	Andy Beck	2025-02-04	wflow_publish("analysis/three_pos_results.Rmd")
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Rmd	7f0e856	Andy Beck	2025-02-04	wflow_publish("analysis/three_pos_results.Rmd")
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Rmd	1c3ffad	Andy Beck	2025-02-04	wflow_publish("analysis/three_pos_results.Rmd")
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Rmd	f2cfb8d	Andy Beck	2025-02-04	wflow_publish("analysis/three_pos_results.Rmd")
html	24d3bdf	Andy Beck	2025-02-04	Build site.
Rmd	603fb4a	Andy Beck	2025-02-04	wflow_publish("analysis/three_pos_results.Rmd")
html	a5d0c43	Andy Beck	2025-02-04	Build site.
Rmd	6904a6e	Andy Beck	2025-02-04	wflow_publish("analysis/three_pos_results.Rmd")
html	e19e401	Andy Beck	2025-02-04	Build site.
Rmd	853231a	Andy Beck	2025-02-04	wflow_publish("analysis/three_pos_results.Rmd")

---

In this document we will evaluate the results from three-way interaction models. Our primary interest is contrasting their strength to single-position and two-way interactions.

Setup

Libraries

library(tidyverse)

── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.4     ✔ readr     2.1.5
✔ forcats   1.0.0     ✔ stringr   1.5.1
✔ ggplot2   3.5.1     ✔ tibble    3.2.1
✔ lubridate 1.9.3     ✔ tidyr     1.3.1
✔ purrr     1.0.2     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

library(ggpubfigs) # functions for color blind friendly palettes

Attaching package: 'ggpubfigs'

The following object is masked from 'package:ggplot2':

    theme_grey

library(reactable)

Paths

base_dir <- "output" 
three_dir <- paste0(base_dir, "/three_pos") # template: base_dir/three_pos/{population}/{subtype}.csv
two_dir <- paste0(base_dir, "/two_pos") # template: base_dir/two_pos/{population}/{subtype}.csv
single_dir <- paste0(base_dir, "/single_pos") # template: base_dir/single_pos/{population}/{subtype}.csv

Data Reading

subtypes <- c("AT_CG", "AT_GC", "AT_TA",
            "GC_AT", "GC_TA", "GC_CG",
            "cpg_GC_AT", "cpg_GC_TA", "cpg_GC_CG")

read_single <- function(res_dir, pop, subtype, tp=FALSE){
  
  f_name <- paste0(res_dir, "/", pop, "/", subtype, ".csv")
  if(tp){
    return(read_csv(f_name, show_col_types = F, col_names = c("dev","singletons","controls","rp1","rp2")))
  }
  return(read_csv(f_name, show_col_types = FALSE))
}

read_all <- function(single_dir, two_dir, three_dir, pop, subtype){
  s_df <- read_single(single_dir, pop, subtype)
  two_df <- read_single(two_dir, pop, subtype, tp=T)
  three_df <- read_single(three_dir, pop, subtype)
  
  # compute re 
  three_df <- three_df %>%
    mutate(re = dev / (2 * (singletons + controls)))
  two_df <- two_df %>%
    mutate(re = dev / (2 * (singletons + controls)))
  s_df <- s_df %>%
    mutate(re = dev / (2 * (singletons + controls)))
  
  # rank by re
  three_df <- three_df %>%
    mutate(class_rank = dense_rank(desc(re)))
  two_df <- two_df %>%
    mutate(class_rank = dense_rank(desc(re)))
  s_df <- s_df %>%
    mutate(class_rank = dense_rank(desc(re)))
  
  # unify structure: dev, offsets, re, class, class_rank
  three_df <- three_df %>%
    rowwise() %>%
    mutate(offset = paste0(rp1, "_", rp2, "_", rp3)) %>%
    ungroup() %>%
    mutate(class = "3-pos") %>%
    select(dev, offset, re, class ,class_rank) 
  
  two_df <- two_df %>%
    mutate(class = "2-pos") %>%
    rowwise() %>%
    mutate(offset = paste0(rp1, "_", rp2)) %>%
    ungroup() %>%
    select(dev, offset, re, class, class_rank)
  
  s_df <- s_df %>%
    mutate(class = "1-pos",
           offset = as.character(offset)) %>%
    select(dev, offset, re, class, class_rank)
  
  final_df <- bind_rows(s_df, two_df, three_df)
  return(final_df)
}

Rank Plots

subtype_print_names <- function(st){
  if(str_starts(st, "AT")){
    return(paste0("A → ", str_sub(st, 4, 4)))
  } else if(str_starts(st, "GC")){
    return(paste0("C → ", str_sub(st, 5, 5)))
  } else{
    return(paste0("CpG → ", str_sub(st, 9, 9), "pG"))
  }
}

# function will print both table and plot
plot_ranked_re <- function(single_dir, two_dir, three_dir, pop, subtype, rank_lim = 20){
  df <- read_all(single_dir, two_dir, three_dir, pop, subtype)
  
  max_re <- max(df$re)
  df$pct_max <- df$re / max_re
  
  p <- df %>%
    filter(class_rank <= rank_lim) %>%
    mutate(class2 = recode(class, "1-pos" = "Single", "2-pos" = "Two-Way", "3-pos" = "Three-Way")) %>%
    ggplot(aes(x = class_rank, y = pct_max, colour = class2, shape = class2)) +
    geom_point(size = 2.5) +
    scale_colour_manual(values=friendly_pal("contrast_three"), name = "Type", breaks=c("Single","Two-Way","Three-Way")) +
    scale_shape_discrete(name = "Type", breaks=c("Single","Two-Way","Three-Way")) +
    theme_classic(base_size = 12, base_family = "Helvetica") +
    theme(legend.position = "inside",
          legend.position.inside = c(.8, .8)) +
    ylab("% of Max RE") +
    xlab(paste0("Within-class Rank: ", subtype_print_names(subtype)))
  return(list(df=df, fig=p))
}

Figures and Tables

Let’s look at mtcars instead of local sequence context non-sense…

reactable(mtcars[1:4, 1:5])

And now that the reactable stuff has been attached to our document, let’s look at local sequence context results :)

ALL

AT_CG

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Version	Author	Date
60bf24e	Andy Beck	2025-02-04

AT_GC

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Version	Author	Date
60bf24e	Andy Beck	2025-02-04

AT_TA

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Version	Author	Date
60bf24e	Andy Beck	2025-02-04

GC_AT

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Version	Author	Date
60bf24e	Andy Beck	2025-02-04

GC_TA

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Version	Author	Date
60bf24e	Andy Beck	2025-02-04

GC_CG

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Version	Author	Date
60bf24e	Andy Beck	2025-02-04

cpg_GC_AT

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Version	Author	Date
60bf24e	Andy Beck	2025-02-04

cpg_GC_TA

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Version	Author	Date
60bf24e	Andy Beck	2025-02-04

cpg_GC_CG

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Version	Author	Date
60bf24e	Andy Beck	2025-02-04

AFR

AT_CG

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

AT_GC

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

AT_TA

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05d7220	Andy Beck	2025-02-04

GC_AT

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

GC_TA

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

GC_CG

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

cpg_GC_AT

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

cpg_GC_TA

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05d7220	Andy Beck	2025-02-04

cpg_GC_CG

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05d7220	Andy Beck	2025-02-04

AMR

AT_CG

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

AT_GC

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

AT_TA

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05d7220	Andy Beck	2025-02-04

GC_AT

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

GC_TA

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

GC_CG

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

cpg_GC_AT

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

cpg_GC_TA

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

cpg_GC_CG

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05d7220	Andy Beck	2025-02-04

EAS

AT_CG

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05d7220	Andy Beck	2025-02-04

AT_GC

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05d7220	Andy Beck	2025-02-04

AT_TA

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

GC_AT

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

GC_TA

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

GC_CG

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

cpg_GC_AT

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

cpg_GC_TA

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

cpg_GC_CG

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05d7220	Andy Beck	2025-02-04

EUR

AT_CG

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05d7220	Andy Beck	2025-02-04

AT_GC

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05d7220	Andy Beck	2025-02-04

AT_TA

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

GC_AT

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

GC_TA

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

GC_CG

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

cpg_GC_AT

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

cpg_GC_TA

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

cpg_GC_CG

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

SAS

AT_CG

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

AT_GC

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

AT_TA

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

GC_AT

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

GC_TA

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

GC_CG

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

cpg_GC_AT

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

cpg_GC_TA

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

cpg_GC_CG

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Version	Author	Date
05d7220	Andy Beck	2025-02-04

Session information

sessionInfo()

R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/New_York
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] reactable_0.4.4 ggpubfigs_0.0.1 lubridate_1.9.3 forcats_1.0.0  
 [5] stringr_1.5.1   dplyr_1.1.4     purrr_1.0.2     readr_2.1.5    
 [9] tidyr_1.3.1     tibble_3.2.1    ggplot2_3.5.1   tidyverse_2.0.0
[13] workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] gtable_0.3.6      xfun_0.49         bslib_0.8.0       htmlwidgets_1.6.4
 [5] processx_3.8.4    callr_3.7.6       tzdb_0.4.0        vctrs_0.6.5      
 [9] tools_4.4.2       crosstalk_1.2.1   ps_1.8.1          generics_0.1.3   
[13] parallel_4.4.2    fansi_1.0.6       pkgconfig_2.0.3   lifecycle_1.0.4  
[17] farver_2.1.2      compiler_4.4.2    git2r_0.33.0      munsell_0.5.1    
[21] getPass_0.2-4     httpuv_1.6.15     htmltools_0.5.8.1 sass_0.4.9       
[25] yaml_2.3.10       later_1.3.2       pillar_1.9.0      crayon_1.5.3     
[29] jquerylib_0.1.4   whisker_0.4.1     cachem_1.1.0      tidyselect_1.2.1 
[33] digest_0.6.37     stringi_1.8.4     labeling_0.4.3    rprojroot_2.0.4  
[37] fastmap_1.2.0     grid_4.4.2        archive_1.1.8     colorspace_2.1-1 
[41] cli_3.6.3         magrittr_2.0.3    utf8_1.2.4        withr_3.0.2      
[45] reactR_0.6.1      scales_1.3.0      promises_1.3.0    bit64_4.6.0-1    
[49] timechange_0.3.0  rmarkdown_2.29    httr_1.4.7        bit_4.5.0.1      
[53] hms_1.1.3         evaluate_1.0.1    knitr_1.49        rlang_1.1.4      
[57] Rcpp_1.0.13-1     glue_1.8.0        rstudioapi_0.17.1 vroom_1.6.5      
[61] jsonlite_1.8.9    R6_2.5.1          fs_1.6.5